def test_h2():
#frequency of H2 stretch mode in gaussian.fchk calculation is 4416.656/cm
#and an equilibrium bond length of 0.7442380 A. This test checks if the
#force field predicts the same values
r0 = 0.7442380*angstrom
freq = (2*np.pi)*4416.65640485*lightspeed/centimeter
mass = pt['H'].mass/2 #reduced mass for the H2 stretch mode
#Load system, model and pert. theory and estimate ff
with log.section('NOSETST', 2):
system, ai = read_system('H2/gaussian.fchk')
set_ffatypes(system, 'low')
program = DeriveFF(system, ai, Settings())
program.do_pt_generate()
program.do_pt_estimate()
K_pt, rv_pt = program.valence.get_params(0, only='all')
program.do_hc_estimatefc(['HC_FC_DIAG'])
K_hc, rv_hc = program.valence.get_params(0, only='all')
#print results
print ''
print 'AI : K = %.3f kjmol/A^2 q0 = %.6f A' %(mass*freq**2/(kjmol/angstrom**2), r0/angstrom)
print 'FF (PT): K = %.3f kjmol/A^2 q0 = %.6f A' %(K_pt/(kjmol/angstrom**2), rv_pt/angstrom)
print 'FF (HC): K = %.3f kjmol/A^2 q0 = %.6f A' %(K_hc/(kjmol/angstrom**2), rv_hc/angstrom)
print ''
#perform assertion checks
assert abs(K_pt/(mass*freq**2)-1.0) < 1e-3
assert abs(rv_pt/r0-1.0) < 1e-3
assert abs(K_hc/(mass*freq**2)-1.0) < 1e-3
assert abs(rv_hc/r0-1.0) < 1e-3
assert abs(K_hc/K_pt-1.0) < 1e-6
assert abs(rv_hc/rv_pt-1.0) < 1e-6
def do_taylor(name, ntests=10, eps=1e-4, gtol=1e-3*kjmol/angstrom, htol=1e-3*kjmol/angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
print('')
for i in range(ntests):
npos = system.pos + np.random.normal(0.0, 0.1, system.pos.shape)*angstrom
gref = ref.gradient(npos)
gnum = np.zeros(3*len(system.numbers), float)
for j in range(3*len(system.numbers)):
dx = np.zeros(3*len(system.numbers), float)
dx[j] = 1.0
dx = dx.reshape(npos.shape)
eplus = ref.energy(npos + eps*dx)
emin = ref.energy(npos - eps*dx)
gnum[j] = (eplus-emin)/(2.0*eps)
std = gref.std()
M = (abs(gref-gnum.reshape(gref.shape))).max()
print(' Sample %i: STD=%.6e MaxDev=%.6e' %(i, std/(kjmol/angstrom), M/(kjmol/angstrom)))
assert M<gtol
for i in range(ntests):
npos = system.pos + np.random.normal(0.0, 0.1, system.pos.shape)*angstrom
href = ref.hessian(npos)
hnum = np.zeros([3*len(system.numbers), 3*len(system.numbers)], float)
for k in range(3*len(system.numbers)):
dx = np.zeros(3*len(system.numbers), float)
dx[k] = 1.0
dx = dx.reshape(npos.shape)
gplus = ref.gradient(npos + eps*dx)
gmin = ref.gradient(npos - eps*dx)
hnum[k,:] = (gplus-gmin).reshape(3*len(system.numbers))/(2.0*eps)
hnum = 0.5*(hnum+hnum.T)
std = href.std()
M = (abs(gref-gnum.reshape(gref.shape))).max()
print(' Sample %i: STD=%.6e MaxDev=%.6e: ' %(i, std/(kjmol/angstrom**2), M/(kjmol/angstrom**2)))
assert M<htol
def check_hessian_bonds(name, tol=1e-3 * kjmol / angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
set_ffatypes(system, 'highest')
valence = ValenceFF(system, Settings())
for term in valence.iter_terms('BONDHARM'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=1.00, high=2.00) * angstrom
fc = np.random.uniform(low=1000, high=3000) * kjmol / angstrom**2
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current bond
#are zero
if len(izero[0]) > 0:
assert (abs(ref[izero])).max() < 1e-12 * kjmol / angstrom**2
assert (abs(num[izero])).max() < 1e-12 * kjmol / angstrom**2
M = (abs(ref - num)).max()
iM, jM = np.where(abs(ref - num) == M)[0][0], np.where(
abs(ref - num) == M)[1][0]
print(
'%25s (random FC=%8.3f kjmol/A^2 RV=%7.3f A ): MaxDev(%2i,%2i)=%.3e kjmol/A^2'
% (term.basename, fc /
(kjmol / angstrom**2), rv / angstrom, iM, jM, M /
(kjmol / angstrom**2)))
assert M < tol
del system, valence, ref, num
def check_hessian_dihedrals(name, tol=1e-3 * kjmol / angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
set_ffatypes(system, 'highest')
valence = ValenceFF(system, Settings())
ref, num = None, None
for term in valence.iter_terms('TORS'):
psi0 = get_dihedral_angle(term, system)
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=0, high=180) * deg #q0
fc = np.random.uniform(low=10, high=50) * kjmol
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current dihedral
#are zero
if len(izero[0]) > 0:
assert (abs(ref[izero])).max() < 1e-12 * kjmol / angstrom**2
assert (abs(num[izero])).max() < 1e-12 * kjmol / angstrom**2
M = (abs(ref - num)).max()
iM, jM = np.where(abs(ref - num) == M)[0][0], np.where(
abs(ref - num) == M)[1][0]
print(
'%25s (eq=%.1f deg random FC=%8.3f kjmol RV=%7.3f deg): MaxDev(%2i,%2i)=%.3e kjmol/A^2'
% (term.basename, psi0 / deg, fc / kjmol, rv / deg, iM, jM, M /
(kjmol / angstrom**2)))
assert M < tol
del system, valence, ref, num
def check_hessian_dihedrals(name, tol=1e-3 * kjmol / angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
guess_ffatypes(system, 'highest')
valence = ValenceFF(system)
for term in valence.iter_terms('TORSION'):
psi0 = get_dihedral_angle(term, system)
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=0, high=180) * deg #q0
fc = np.random.uniform(low=10, high=50) * kjmol
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current dihedral
#are zero
if len(izero[0]) > 0:
assert (abs(ref[izero])).max() < 1e-12 * kjmol / angstrom**2
assert (abs(num[izero])).max() < 1e-12 * kjmol / angstrom**2
M = (abs(ref - num)).max()
iM, jM = np.where(abs(ref - num) == M)[0][0], np.where(
abs(ref - num) == M)[1][0]
print '%25s (eq=%.1f deg random FC=%8.3f kjmol RV=%7.3f deg): MaxDev(%2i,%2i)=%.3e kjmol/A^2' % (
term.basename, psi0 / deg, fc / kjmol, rv / deg, iM, jM, M /
(kjmol / angstrom**2))
if abs(abs(psi0) - 180 * deg) < 1 * deg or abs(psi0) < 1 * deg:
print ' ==> SKIPPED due to instable numerical implementation of derivatives in Yaff for values dihedrals to 0 or 180 deg'
else:
assert M < tol
del system, valence, ref, num
def check_terms(name):
'Check whether all ICs are present in ValenceFF instance'
#TODO: CROSS terms
with log.section('NOSETST', 2):
system, ref = read_system(name)
guess_ffatypes(system, 'high')
valence = ValenceFF(system)
#check if every bond is present and harmonic
for bond in system.iter_bonds():
found = False
for term in valence.iter_terms('BONDHARM'):
at0, at1 = term.get_atoms()
if bond[0]==at0 and bond[1]==at1 \
or bond[0]==at1 and bond[1]==at0:
assert not found, 'BondHarm term %s was already found!' % str(
bond)
found = True
assert found, 'No BondHarm term found for bond %s' % str(bond)
#check if every bend is present
for angle in system.iter_angles():
found = False
for term in valence.iter_terms('BENDAHARM'):
at0, at1, at2 = term.get_atoms()
if angle[0]==at0 and angle[1]==at1 and angle[2]==at2 \
or angle[0]==at2 and angle[1]==at1 and angle[2]==at0:
assert not found, 'BendAHarm term %s was already found!' % str(
angle)
found = True
assert found, 'No BendAHarm term found for bond %s' % str(angle)
#check if every dihedral is present
for dihed in system.iter_dihedrals():
found = False
for term in valence.iter_terms('TORSION'):
at0, at1, at2, at3 = term.get_atoms()
if dihed[0]==at0 and dihed[1]==at1 and dihed[2]==at2 and dihed[3]==at3\
or dihed[0]==at3 and dihed[1]==at2 and dihed[2]==at1 and dihed[3]==at0:
assert not found, 'Torsion term %s was already found!' % str(
dihed)
found = True
assert found, 'No Torsion term found for bond %s' % str(dihedral)
#check if every oop distance is present and Harm for rv of 0 and SQHARM else
for oop in system.iter_oops():
found = False
for term in valence.iter_terms('/OOPDIST'):
at0, at1, at2, at3 = term.get_atoms()
for p0, p1, p2 in permutations([at0, at1, at2]):
if oop[0] == p0 and oop[1] == p1 and oop[2] == p2 and oop[
3] == at3:
assert not found, 'OopDist term %s was already found!' % str(
oop)
found = True
for term in valence.iter_terms('SQOOPDIST'):
at0, at1, at2, at3 = term.get_atoms()
for p0, p1, p2 in permutations([at0, at1, at2]):
if oop[0] == p0 and oop[1] == p1 and oop[2] == p2 and oop[
3] == at3:
assert not found, 'SqOopDist term %s was already found!' % str(
oop)
found = True
assert found, 'No (Sq)OopDist term found for bond %s' % str(oop)
def test_h2():
#frequency of H2 stretch mode in gaussian.fchk calculation is 4416.656/cm
#and an equilibrium bond length of 0.7442380 A. This test checks if the
#force field predicts the same values
r0 = 0.7442380*angstrom
freq = (2*np.pi)*4416.65640485*lightspeed/centimeter
mass = pt['H'].mass/2 #reduced mass for the H2 stretch mode
#Load system, model and pert. theory and estimate ff
with log.section('NOSETST', 2):
system, ai = read_system('H2/gaussian.fchk')
set_ffatypes(system, 'low')
program = DeriveFF(system, ai, Settings())
program.do_pt_generate()
program.do_pt_estimate()
K_pt, rv_pt = program.valence.get_params(0, only='all')
program.do_hc_estimatefc(['HC_FC_DIAG'])
K_hc, rv_hc = program.valence.get_params(0, only='all')
#print results
print('')
print('AI : K = %.3f kjmol/A^2 q0 = %.6f A' %(mass*freq**2/(kjmol/angstrom**2), r0/angstrom))
print('FF (PT): K = %.3f kjmol/A^2 q0 = %.6f A' %(K_pt/(kjmol/angstrom**2), rv_pt/angstrom))
print('FF (HC): K = %.3f kjmol/A^2 q0 = %.6f A' %(K_hc/(kjmol/angstrom**2), rv_hc/angstrom))
print('')
#perform assertion checks
assert abs(K_pt/(mass*freq**2)-1.0) < 1e-3
assert abs(rv_pt/r0-1.0) < 1e-3
assert abs(K_hc/(mass*freq**2)-1.0) < 1e-3
assert abs(rv_hc/r0-1.0) < 1e-3
assert abs(K_hc/K_pt-1.0) < 1e-6
assert abs(rv_hc/rv_pt-1.0) < 1e-6
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def check_terms(name):
'Check whether all ICs are present in ValenceFF instance'
#TODO: CROSS terms
with log.section('NOSETST', 2):
system, ref = read_system(name)
set_ffatypes(system, 'high')
valence = ValenceFF(system, Settings())
#check if every bond is present and harmonic
for bond in system.iter_bonds():
found = False
for term in valence.iter_terms('BONDHARM'):
at0, at1 = term.get_atoms()
if bond[0]==at0 and bond[1]==at1 \
or bond[0]==at1 and bond[1]==at0:
assert not found, 'BondHarm term %s was already found!' %str(bond)
found = True
assert found, 'No BondHarm term found for bond %s' %str(bond)
#check if every bend is present
for angle in system.iter_angles():
found = False
for term in valence.iter_terms('BENDAHARM'):
at0, at1, at2 = term.get_atoms()
if angle[0]==at0 and angle[1]==at1 and angle[2]==at2 \
or angle[0]==at2 and angle[1]==at1 and angle[2]==at0:
assert not found, 'BendAHarm term %s was already found!' %str(angle)
found = True
assert found, 'No BendAHarm term found for bond %s' %str(angle)
#check if every dihedral is present
for dihed in system.iter_dihedrals():
found = False
for term in valence.iter_terms('Tors'):
at0, at1, at2, at3 = term.get_atoms()
if dihed[0]==at0 and dihed[1]==at1 and dihed[2]==at2 and dihed[3]==at3\
or dihed[0]==at3 and dihed[1]==at2 and dihed[2]==at1 and dihed[3]==at0:
assert not found, 'Torsion term %s was already found!' %str(dihed)
found = True
assert found, 'No Torsion term found for bond %s' %str(dihed)
#check if every oop distance is present and Harm for rv of 0 and SQHARM else
for oop in system.iter_oops():
found = False
for term in valence.iter_terms('^OOPDIST/.*$', use_re=True):
at0, at1, at2, at3 = term.get_atoms()
for p0, p1, p2 in permutations([at0, at1, at2]):
if oop[0]==p0 and oop[1]==p1 and oop[2]==p2 and oop[3]==at3:
assert not found, 'OopDist term %s was already found!' %str(oop)
found = True
for term in valence.iter_terms('SQOOPDIST'):
at0, at1, at2, at3 = term.get_atoms()
for p0, p1, p2 in permutations([at0, at1, at2]):
if oop[0]==p0 and oop[1]==p1 and oop[2]==p2 and oop[3]==at3:
assert not found, 'SqOopDist term %s was already found!' %str(oop)
found = True
assert found, 'No (Sq)OopDist term found for bond %s (which is %s)' %(
str(oop),
' '.join([system.ffatypes[system.ffatype_ids[i]] for i in [at0,at1,at2,at3]])
)
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir('test_methane_%s'%('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,fn_sys=fn_sys,do_cross_DSS=True,do_cross_DSD=True,
do_cross_DAA=True,do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program,equal=consistent)
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],
data['pos'],
charges=data['charges'],
ffatypes=data['ffatypes'],
bonds=data['bonds'],
radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai',
coords=system.pos.copy(),
grad=data['gradient'],
hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(
system, ai,
Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,
fn_yaff=fn_yaff,
fn_sys=fn_sys,
log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s" % ("Basename", "Cross FC", "Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0, 1]:
fc_diag = program.valence.get_params(
term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" %
(term.basename, fc, fc_diag, program.valence.terms[
term.diag_term_indexes[i]].basename))
if fc_diag == 0.0: assert fc == 0.0
def check_hessian_oops(name, tol=1e-3 * kjmol / angstrom**2):
with log.section('PROGRAM', 2):
system, ref = read_system(name)
guess_ffatypes(system, 'highest')
valence = ValenceFF(system)
for term in valence.iter_terms('/OOPDIST'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = 0.0
fc = np.random.uniform(low=500, high=5000) * kjmol / angstrom**2
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current oop
#are zero
if len(izero[0]) > 0:
assert (abs(ref[izero])).max() < 1e-12 * kjmol / angstrom**2
assert (abs(num[izero])).max() < 1e-12 * kjmol / angstrom**2
M = (abs(ref - num)).max()
iM, jM = np.where(abs(ref - num) == M)[0][0], np.where(
abs(ref - num) == M)[1][0]
print '%25s (random FC=%8.3f kjmol/A^2 RV=%7.3f A ): MaxDev(%2i,%2i)=%.3e kjmol/A^2' % (
term.basename, fc /
(kjmol / angstrom**2), rv / angstrom, iM, jM, M /
(kjmol / angstrom**2))
assert M < tol
for term in valence.iter_terms('SQOOPDIST'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=0.01, high=0.1) * angstrom**2
fc = np.random.uniform(low=500, high=5000) * kjmol / angstrom**4
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current oop
#are zero
if len(izero[0]) > 0:
assert (abs(ref[izero])).max() < 1e-12 * kjmol / angstrom**2
assert (abs(num[izero])).max() < 1e-12 * kjmol / angstrom**2
M = (abs(ref - num)).max()
iM, jM = np.where(abs(ref - num) == M)[0][0], np.where(
abs(ref - num) == M)[1][0]
print '%25s (random FC=%8.3f kjmol/A^4 RV=%7.3f A^2): MaxDev(%2i,%2i)=%.3e kjmol/A^2' % (
term.basename, fc /
(kjmol / angstrom**4), rv / angstrom**2, iM, jM, M /
(kjmol / angstrom**2))
assert M < tol
del system, valence, ref, num
def check_hessian_bends(name, tol=1e-3*kjmol/angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
set_ffatypes(system, 'highest')
valence = ValenceFF(system, Settings())
for term in valence.iter_terms('BENDAHARM'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=10, high=170)*deg
fc = np.random.uniform(low=100, high=1000)*kjmol/rad**2
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current bend
#are zero
if len(izero[0])>0:
assert (abs(ref[izero])).max()<1e-12*kjmol/angstrom**2
assert (abs(num[izero])).max()<1e-12*kjmol/angstrom**2
M = (abs(ref-num)).max()
iM, jM = np.where(abs(ref-num)==M)[0][0], np.where(abs(ref-num)==M)[1][0]
print('%25s (random FC=%8.3f kjmol/rad^2 RV=%7.3f deg): MaxDev(%2i,%2i)=%.3e kjmol/A^2' %(term.basename, fc/(kjmol/rad**2), rv/deg, iM, jM, M/(kjmol/angstrom**2)))
assert M<tol
del system, valence, ref, num
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir(
'test_methane_%s' %
('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(
system, ai,
Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,
fn_sys=fn_sys,
do_cross_DSS=True,
do_cross_DSD=True,
do_cross_DAA=True,
do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program, equal=consistent)
def check_hessian_oops(name, tol=1e-3*kjmol/angstrom**2):
with log.section('PROGRAM', 2):
system, ref = read_system(name)
set_ffatypes(system, 'highest')
valence = ValenceFF(system, Settings())
for term in valence.iter_terms('/OOPDIST'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = 0.0
fc = np.random.uniform(low=500, high=5000)*kjmol/angstrom**2
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current oop
#are zero
if len(izero[0])>0:
assert (abs(ref[izero])).max()<1e-12*kjmol/angstrom**2
assert (abs(num[izero])).max()<1e-12*kjmol/angstrom**2
M = (abs(ref-num)).max()
iM, jM = np.where(abs(ref-num)==M)[0][0], np.where(abs(ref-num)==M)[1][0]
print('%25s (random FC=%8.3f kjmol/A^2 RV=%7.3f A ): MaxDev(%2i,%2i)=%.3e kjmol/A^2' %(
term.basename, fc/(kjmol/angstrom**2), rv/angstrom, iM, jM, M/(kjmol/angstrom**2)
))
assert M<tol
del ref, num
for term in valence.iter_terms('SQOOPDIST'):
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=0.01, high=0.1)*angstrom**2
fc = np.random.uniform(low=500, high=5000)*kjmol/angstrom**4
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current oop
#are zero
if len(izero[0])>0:
assert (abs(ref[izero])).max()<1e-12*kjmol/angstrom**2
assert (abs(num[izero])).max()<1e-12*kjmol/angstrom**2
M = (abs(ref-num)).max()
iM, jM = np.where(abs(ref-num)==M)[0][0], np.where(abs(ref-num)==M)[1][0]
print('%25s (random FC=%8.3f kjmol/A^4 RV=%7.3f A^2): MaxDev(%2i,%2i)=%.3e kjmol/A^2' %(term.basename, fc/(kjmol/angstrom**4), rv/angstrom**2, iM, jM, M/(kjmol/angstrom**2)))
assert M<tol
del ref, num
del system, valence
def check_hessian_dihedrals(name, tol=1e-3*kjmol/angstrom**2):
with log.section('NOSETST', 2):
system, ref = read_system(name)
set_ffatypes(system, 'highest')
valence = ValenceFF(system, Settings())
ref, num = None, None
for term in valence.iter_terms('TORS'):
psi0 = get_dihedral_angle(term, system)
inonzero, izero = get_indices_zero_nonzero(term, len(system.numbers))
rv = np.random.uniform(low=0, high=180)*deg #q0
fc = np.random.uniform(low=10, high=50)*kjmol
ref, num = get_analytic_numeric_hessian(valence, term, fc=fc, rv0=rv)
#assert that hessian elements of atoms not part of the current dihedral
#are zero
if len(izero[0])>0:
assert (abs(ref[izero])).max()<1e-12*kjmol/angstrom**2
assert (abs(num[izero])).max()<1e-12*kjmol/angstrom**2
M = (abs(ref-num)).max()
iM, jM = np.where(abs(ref-num)==M)[0][0], np.where(abs(ref-num)==M)[1][0]
print('%25s (eq=%.1f deg random FC=%8.3f kjmol RV=%7.3f deg): MaxDev(%2i,%2i)=%.3e kjmol/A^2' %(
term.basename, psi0/deg, fc/kjmol, rv/deg, iM, jM, M/(kjmol/angstrom**2)
))
assert M<tol
del system, valence, ref, num
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print line
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 2
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert f.next() == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in xrange(natom+1):
f.next()
line = f.next()
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nbond*2
f.next()
line = f.next()
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == ntheta*3
f.next()
line = f.next()
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nphi*4
f.next()
line = f.next()
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print(line)
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 3
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert next(f) == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in range(natom+1):
next(f)
line = next(f)
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nbond*2
next(f)
line = next(f)
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == ntheta*3
next(f)
line = next(f)
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nphi*4
next(f)
line = next(f)
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0
